A properly built mod will not require you to upload individual files, especially if they are in a folder structure already. I presume the two folders are for alternative situations, and only one is intended to be used in any one case. The author could shed more light on this.

Keeping original files renamed in the original locations can sometimes be a problem, as some folders are auto-loading - every file in them will be used. In nearly all cases, if you use the template override system, the original copy of the file is safe in the /template_default/ folder so there is no need to save another copy.
If you are not using the override system, you are setting yourself up for a lot of grief when the next version comes out and you try to upgrade.

For a mod like this that deals with /admin/ files, you do need to replace the originals, so keeping a backup copy elsewhere would be good.